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Officials in the Boston public schools learned as early as 2004 that their embattled food service system lacked adequate inventory controls, a problem highlighted in an internal report warning that the School Department needed substantial reforms.

Those inventory problems took on grave significance yesterday as school officials admitted during a City Council hearing that students had recently been served eggs and ground beef that had been frozen as long as two years.

Facing a scathing critique of the department’s food services, Superintendent Carol R. Johnson and other top school officials acknowledged significant problems with inventory and menus, but defended the quality of the meals and highlighted strides made by the food service in recent years.

“Let’s be clear, the food we serve to our students is safe; all the food is safe,’’ said Johnson, who took over in 2007. “Our managers and kitchen staff would never serve anything that they would not serve to their own families.’’

On Monday, the School Department reassigned its longtime director of food and nutrition services amid revelations it had out-of-date food in freezers. The 2004 report, provided upon request from the School Department, had urged the department to overhaul its inventory tracking system.

That report was written by Leif Dormsjo, a summer policy fellow at the Harvard Kennedy School, for John McDonough, the school’s chief financial officer. It noted that “poor accountability controls have contributed to the financial problems.’’ It said the food service had “separate systems for its purchasing, inventory, sales, expenses, transportation, and staffing’’ that were not integrated.

“The department must incorporate more real-time tracking tools into the day-to-day management of the operation,’’ wrote Dormsjo, who now works for the Maryland Department of Transportation. He declined to discuss his work for the Boston public schools.

A subsequent state audit of Boston’s cafeterias in 2009 did not find any substantial violations, but noted that “inventory records are formatted differently for each school.’’

Neither report was mentioned yesterday in the City Council chambers. However, the hearing cast a spotlight on an aging food service that has struggled for some time with costs and management. Two years ago the department faced a deficit that threatened to hit $6.7 million before cuts and organizational changes significantly lowered costs.

The latest round of concerns came to the public’s attention when Councilor at Large John R. Connolly made a surprise visit to four cafeterias and discovered out of date food, much of it in freezers. US Department of Agriculture guidelines say that properly frozen food can remain safe after expiration dates, but that it can deteriorate in taste and nutritional value.

Connolly pressed Shamil Mohammed, the new interim director of food and nutrition services, to explain why grilled egg patties frozen since 2009 ended up onthis week’s breakfast menu. Menus were printed in advance, Mohammed said, and the grilled egg patties have been pulled out of cafeterias.

“It’s an issue of inventory control and menu planning,’’ said Mohammed. “I’m not defending this; I’m just trying to explain what occurred.’’

The School Department has pulled 280 cases worth of old food out of 40 of its 46 cafeterias with full kitchens. At a supply warehouse in Wilmington, the department also set aside another 3,049 cases of food because records do not readily show expiration dates or “best-if-used-by’’ dates.

Officials have been peeling away plastic packaging on the pallets, looking for dates or other clues to how long the food has been in storage. While school officials vowed to discard out-of-date food and make immediate changes, they noted that items in question are worth roughly $114,000, which represents less than 1 percent of the department’s annual food budget.

The former director, Helen Mont-Ferguson, who was paid $116,029 in 2010 and has run the food service since 1988, was reassigned elsewhere in the School Department, but not terminated.

Officials noted Boston schools have worked in the last decade to improve school food offerings. In 2004, they banned soda and pushed its supplier to lower the sugar in its fat-free chocolate milk. Daily menus appear online, allowing parents to monitor nutritional information.